Calmodulin-dependent protein kinase IV (CaM-kinase IV), which plays crucial roles in the functioning of Ca2+ in the central nervous and immune systems, is markedly activated upon phosphorylation through the action of CaM-kinase kinase. Our previous immunotitration analysis suggested the existence of an isoform different from CaM-kinase kinase alpha, the beta isoform, in rat brain [Okuno, S., Kitani, T., and Fujisawa, H. (1996) J. Biochem. 119, 1176-1181]. In the present study, cDNA for CaM-kinase kinase beta was cloned from a rat cerebellar cDNA library. The coded protein consisted of 587 amino acids with a molecular weight of 64,445. Western blot analysis revealed that CaM-kinase kinase beta significantly existed only in the brain. The enzyme was not significantly detected in the retina where CaM-kinase kinase alpha exists.